Feezing after Restart or Shut Down commands

Perhaps this is a common problem, as I have seen it happen before, but I have a Mac G5 in my lab that, after being told to restart, or shut down, the icons disappear like normal, but it just sits there with the desktop background up. No shut down, no restart.
I can restart manually by holding down the power button, but this machine is the master image for the lab and has to be able to shut down by timer, due to our college's "green" policies. If it won;t shut down on it's own, and has to be done manually, it defeats the purpose.
I've already resatrted from the CD and ran Disk Utility to repair and verify permissions. It did find errors, and said it fixed them, but after restarting from the hard drive again, it is still freezing after given the shut down or restart commands. The cursor still moves and the desktop background are there, just no icons or dock.
Any help is greatly appreciated!

Hi-
The power functions of the machine are controlled by the PMU/SMU.
A reset may be what is needed.
http://support.apple.com/kb/HT1939
http://support.apple.com/kb/HT1436

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Feezing after Restart or Shut Down commands

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